The source code for building the
programs is bundled in the
hssp project. The mkhssp executable
creates stockholm files with hssp annotations in them. The hsspconv
executable converts stockholm to the original hssp format.
The provided Dockerfile sets up a development environment. Build the docker
image using the command
docker build -t hssp . and run the image in a
container, with a local source copy and data files mounted, with the command
docker run -v /home/jon/projects/hssp:/app -v /mnt/extra:/srv/data -it hssp.
Download and installation instructions
Source code archives are available here.
Compiling hssp programs
- Must support at least the c++ 11 standard.
- libzeep version >= 3.0 (for mkhssp --fetch-dbrefs only)
- libboost version >= 1.48
Download and uncompress the hssp source code archive (version >= 2.2.6):
wget https://github.com/cmbi/hssp/archive/hssp-?.?.?.tar.gz tar -zxvf hssp-?.?.?.tar.gz cd hssp-?.?.?
Configure and build the hssp executables:
./autogen.sh ./configure make
To build only one executable of the hssp project, e.g.
To test the
mkhssp executable type:
To add the executables to /usr/local/bin type:
sudo make install
The reference for the new versions of hssp and other protein structure bioinformatics facilities is:
A series of PDB-related databanks for everyday needs Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, E. Krieger, Robbie P. Joosten and Gert Vriend. Nucl. Acids Res. (2015) 43, D364-D368
The original reference for DSSP is:
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W and Sander C, Biopolymers (1983) 22, 2577-2637.
The original reference for HSSP is:
Database of homology-derived protein structures and the structural meaning of sequence alignment. Sander C and Schneider R, Proteins (1991) 9, 56-68.
In 2013, maintenance of hssp has been taken over from Maarten Hekkelman by Coos Baakman. If you want to provide feedback, either send an e-mail to email@example.com or have a look at existing issues (if necessary, create a new issue).